This will count the matching characters. 
my $orig = <DATA>;

my $i = 0;
while (<DATA>) {
    my $matches = $orig ^ $_;
    printf "Sequence %d has %d identities\n", $i++, $matches =~ tr/\0/
+/;    
}

__DATA__
ATCGGGACG 
TCGTCAGCG
ATGCGAAAA

[download]
Prints: 
Sequence 0 has 2 identities
Sequence 1 has 4 identities

[download]

In reply to Re: Compare two variables by Cristoforo
in thread Compare two variables by dmunoze

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